SPMUtilities/AFM_thumbs
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KPFM 2 omega signal 'KPFM_2w'. It is an added signal in list of channels. Nanonis adaption.

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This commit is contained in:
Clemens Barth
2022-04-08 22:21:14 +02:00
parent bb66cd7460
commit 753fe29502
7 changed files with 18 additions and 54 deletions
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49
AFM_thumbs/Channel.py
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@@ -38,34 +38,26 @@ def rename_channel(name):
if re.search(ID_list[0],name):
globvar_AFMdata.channel.append("Topography")
elif re.search(ID_list[4],name):
if re.search(ID_list[5],name):
globvar_AFMdata.channel.append("filtered df")
else:
globvar_AFMdata.channel.append("df")
elif re.search(ID_list[1],name):
globvar_AFMdata.channel.append("Amplitude")
elif re.search(ID_list[6],name):
globvar_AFMdata.channel.append("Dissipation")
elif re.search(ID_list[2],name):
if re.search(ID_list[3],name):
globvar_AFMdata.channel.append("Kelvin Error")
else:
globvar_AFMdata.channel.append("Kelvin")
elif re.search(ID_list[8],name):
globvar_AFMdata.channel.append("Ext 1")
elif re.search(ID_list[9],name):
globvar_AFMdata.channel.append("Ext 2")
elif re.search(ID_list[7],name):
globvar_AFMdata.channel.append("Excitation")
elif re.search(ID_list[10],name):
globvar_AFMdata.channel.append("Phase")
else:
@@ -91,51 +83,43 @@ def proceed_with(image_nr,direction):
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[1]:
return True
elif globvar_AFMdata.channel[image_nr] == "df":
if not globvar_AFMdata.channel[image_nr] == "filtered":
if direction == "forward" and globvar_ThumbPara.thumbs[2]:
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[3]:
return True
elif globvar_AFMdata.channel[image_nr] == "Dissipation":
if direction == "forward" and globvar_ThumbPara.thumbs[4]:
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[5]:
return True
elif globvar_AFMdata.channel[image_nr] == "Amplitude":
if direction == "forward" and globvar_ThumbPara.thumbs[6]:
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[7]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin":
if not globvar_AFMdata.channel[image_nr] == "Error":
if direction == "forward" and globvar_ThumbPara.thumbs[8]:
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[9]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
if direction == "forward" and globvar_ThumbPara.thumbs[10]:
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[11]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 1":
if direction == "forward" and globvar_ThumbPara.thumbs[12]:
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[13]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 2":
if direction == "forward" and globvar_ThumbPara.thumbs[14]:
return True
elif direction == "backward" and globvar_ThumbPara.thumbs[15]:
return True
else:
for i, chan in enumerate(globvar_ThumbPara.channel_names):
if not chan == "":
@@ -157,49 +141,41 @@ def line_fit(image_nr,direction):
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[1]:
return True
elif globvar_AFMdata.channel[image_nr] == "df":
if direction == "forward" and globvar_ThumbPara.line_fit[2]:
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[3]:
return True
elif globvar_AFMdata.channel[image_nr] == "Dissipation":
if direction == "forward" and globvar_ThumbPara.line_fit[4]:
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[5]:
return True
elif globvar_AFMdata.channel[image_nr] == "Amplitude":
if direction == "forward" and globvar_ThumbPara.line_fit[6]:
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[7]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin":
if direction == "forward" and globvar_ThumbPara.line_fit[8]:
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[9]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
if direction == "forward" and globvar_ThumbPara.line_fit[10]:
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[11]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 1":
if direction == "forward" and globvar_ThumbPara.line_fit[12]:
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[13]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 2":
if direction == "forward" and globvar_ThumbPara.line_fit[14]:
return True
elif direction == "backward" and globvar_ThumbPara.line_fit[15]:
return True
else:
for i, chan in enumerate(globvar_ThumbPara.channel_names):
if not chan == "":
@@ -221,49 +197,41 @@ def plane_fit(image_nr,direction):
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[1]:
return True
elif globvar_AFMdata.channel[image_nr] == "df":
if direction == "forward" and globvar_ThumbPara.plane_fit[2]:
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[3]:
return True
elif globvar_AFMdata.channel[image_nr] == "Dissipation":
if direction == "forward" and globvar_ThumbPara.plane_fit[4]:
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[5]:
return True
elif globvar_AFMdata.channel[image_nr] == "Amplitude":
if direction == "forward" and globvar_ThumbPara.plane_fit[6]:
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[7]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin":
if direction == "forward" and globvar_ThumbPara.plane_fit[8]:
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[9]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
if direction == "forward" and globvar_ThumbPara.plane_fit[10]:
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[11]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 1":
if direction == "forward" and globvar_ThumbPara.plane_fit[12]:
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[13]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 2":
if direction == "forward" and globvar_ThumbPara.plane_fit[14]:
return True
if direction == "backward" and globvar_ThumbPara.plane_fit[15]:
return True
else:
for i, chan in enumerate(globvar_ThumbPara.channel_names):
if not chan == "":
@@ -285,55 +253,46 @@ def invert(image_nr,direction):
direction = "forward"
elif image_nr%2 != 0:
direction = "backward"
if globvar_AFMdata.channel[image_nr] == "Topography":
if direction == "forward" and globvar_ThumbPara.invert[0]:
return True
if direction == "backward" and globvar_ThumbPara.invert[1]:
return True
elif globvar_AFMdata.channel[image_nr] == "df":
if direction == "forward" and globvar_ThumbPara.invert[2]:
return True
if direction == "backward" and globvar_ThumbPara.invert[3]:
return True
elif globvar_AFMdata.channel[image_nr] == "Dissipation":
if direction == "forward" and globvar_ThumbPara.invert[4]:
return True
if direction == "backward" and globvar_ThumbPara.invert[5]:
return True
elif globvar_AFMdata.channel[image_nr] == "Amplitude":
if direction == "forward" and globvar_ThumbPara.invert[6]:
return True
if direction == "backward" and globvar_ThumbPara.invert[7]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin":
if direction == "forward" and globvar_ThumbPara.invert[8]:
return True
if direction == "backward" and globvar_ThumbPara.invert[9]:
return True
elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
if direction == "forward" and globvar_ThumbPara.invert[10]:
return True
if direction == "backward" and globvar_ThumbPara.invert[11]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 1":
if direction == "forward" and globvar_ThumbPara.invert[12]:
return True
if direction == "backward" and globvar_ThumbPara.invert[13]:
return True
elif globvar_AFMdata.channel[image_nr] == "Ext 2":
if direction == "forward" and globvar_ThumbPara.invert[14]:
return True
if direction == "backward" and globvar_ThumbPara.invert[15]:
return True
else:
for i, chan in enumerate(globvar_ThumbPara.channel_names):
if not chan == "":
@@ -364,49 +323,41 @@ def select_color(image_nr,direction):
direction = "forward"
elif image_nr%2 != 0:
direction = "backward"
if globvar_AFMdata.channel[image_nr] == "Topography":
if direction == "forward":
return globvar_ThumbPara.colors[0]
if direction == "backward":
return globvar_ThumbPara.colors[1]
elif globvar_AFMdata.channel[image_nr] == "df":
if direction == "forward":
return globvar_ThumbPara.colors[2]
if direction == "backward":
return globvar_ThumbPara.colors[3]
elif globvar_AFMdata.channel[image_nr] == "Dissipation":
if direction == "forward":
return globvar_ThumbPara.colors[4]
if direction == "backward":
return globvar_ThumbPara.colors[5]
elif globvar_AFMdata.channel[image_nr] == "Amplitude":
if direction == "forward":
return globvar_ThumbPara.colors[6]
if direction == "backward":
return globvar_ThumbPara.colors[7]
elif globvar_AFMdata.channel[image_nr] == "Kelvin":
if direction == "forward":
return globvar_ThumbPara.colors[8]
if direction == "backward":
return globvar_ThumbPara.colors[9]
elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
if direction == "forward":
return globvar_ThumbPara.colors[10]
if direction == "backward":
return globvar_ThumbPara.colors[11]
elif globvar_AFMdata.channel[image_nr] == "Ext 1":
if direction == "forward":
return globvar_ThumbPara.colors[12]
if direction == "backward":
return globvar_ThumbPara.colors[13]
elif globvar_AFMdata.channel[image_nr] == "Ext 2":
if direction == "forward":
return globvar_ThumbPara.colors[14]

15
AFM_thumbs/Config_default.conf
View File

@@ -48,13 +48,14 @@ File extension :
Direction : 0
Linefit : 3
Planefit : 3
AddChannel : 20
ChannelNumber : 4
AddChannel : 22
ChannelNumber : 5
Tooltips : 0
Channelname 1 : FN
Channelname 2 : FL
Channelname 3 : I
Channelname 4 : Phase
Channelname 5 : KPFM_2w
Thumb 1 : 1
Thumb 2 : 1
Thumb 3 : 1
@@ -79,6 +80,8 @@ Thumb 21 : 1
Thumb 22 : 1
Thumb 23 : 1
Thumb 24 : 1
Thumb 25 : 1
Thumb 26 : 1
LineFit 1 : 1
LineFit 2 : 1
LineFit 3 : 1
@@ -103,6 +106,8 @@ LineFit 21 : 1
LineFit 22 : 1
LineFit 23 : 1
LineFit 24 : 1
LineFit 25 : 1
LineFit 26 : 1
PlaneFit 1 : 0
PlaneFit 2 : 0
PlaneFit 3 : 0
@@ -127,6 +132,8 @@ PlaneFit 21 : 0
PlaneFit 22 : 0
PlaneFit 23 : 0
PlaneFit 24 : 0
PlaneFit 25 : 0
PlaneFit 26 : 0
Inverted 1 : 0
Inverted 2 : 0
Inverted 3 : 1
@@ -151,6 +158,8 @@ Inverted 21 : 0
Inverted 22 : 0
Inverted 23 : 0
Inverted 24 : 0
Inverted 25 : 0
Inverted 26 : 0
Color 1 : Gist_heat
Color 2 : Gist_heat
Color 3 : Grey
@@ -175,3 +184,5 @@ Color 21 : Ocean
Color 22 : Ocean
Color 23 : Grey
Color 24 : Grey
Color 25 : Grey
Color 26 : Grey

5
AFM_thumbs/SPECS_Nanonis.py
View File

@@ -198,7 +198,6 @@ def read_SPECS_Nanonis_image_data(nanonis_file):
# The channels with the following names are not supported.
#
# Bias
# Laser_power_mon.
# Laser_Setpoint
# Output_3
# Output_4
@@ -206,7 +205,6 @@ def read_SPECS_Nanonis_image_data(nanonis_file):
# Y
# Output_8
channels_not_supported = ["Bias",
"Laser_power_mon.",
"Laser_Setpoint",
"Output_3",
"Output_4",
@@ -246,6 +244,8 @@ def read_SPECS_Nanonis_image_data(nanonis_file):
channel_name = "Kelvin"
if channel_name == "KPFM_err":
channel_name = "KELVIN_ERR"
if channel_name == "Laser_power_mon.":
channel_name = "KPFM_2w"
globvar_AFMdata.scandir.append("forward")
globvar_AFMdata.scandir.append("backward")
@@ -326,6 +326,7 @@ def prepare_SPECS_Nanonis_images(nanonis_file, data_offset):
# The definition 'proceed_with' is 'connected' with the GUI of
# AFM_thumbs where one can choose if a channel of a specific
# scanning direction shall be represented in a pdf file or not.
if proceed_with(image_nr,globvar_AFMdata.scandir[image_nr]):
# Prepare the file path.

3
AFM_thumbs/Variables.py
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@@ -288,7 +288,8 @@ ID_abbreviations = {"Topography" : "Z", "filtered df":"df_fil", "Amplitude":"A",
"Dissipation": "D", "Kelvin Error": "KPFM_err",
"Ext 1": "Ext1", "Ext 2": "Ext2", "Excitation": "A_ext",
"Phase": "Phase", "Kelvin": "KPFM", "DF_DIG": "df",
"EXT": "Ext", "EXT1": "Ext1", "EXT2": "Ext2"}
"EXT": "Ext", "EXT1": "Ext1", "EXT2": "Ext2",
"Kelvin_2w": "KPFM2w"}
# ______________________________________________________________________ Colors

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AFM_thumbs/__pycache__/Channel.cpython-38.pyc
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AFM_thumbs/__pycache__/SPECS_Nanonis.cpython-38.pyc
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AFM_thumbs/__pycache__/Variables.cpython-38.pyc
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